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Sharon Huws - One of the best experts on this subject based on the ideXlab platform.
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can Rumen Bacteria communicate to each other
Microbiome, 2020Co-Authors: Miyoung Won, Christopher J Creevey, Linda Oyama, Stephen J Courtney, Sharon HuwsAbstract:The Rumen contains a myriad of microbes whose primary role is to degrade and ferment dietary nutrients, which then provide the host with energy and nutrients. Rumen microbes commonly attach to ingested plant materials and form biofilms for effective plant degradation. Quorum sensing (QS) is a well-recognised form of Bacterial communication in most biofilm communities, with homoserine lactone (AHL)-based QS commonly being used by Gram-negative Bacteria alone and AI-2 Lux-based QS communication being used to communicate across Gram-negative and Gram-positive Bacteria. However, Bacterial cell to cell communication in the Rumen is poorly understood. In this study, Rumen Bacterial genomes from the Hungate collection and Genbank were prospected for QS-related genes. To check that the discovered QS genes are actually expressed in the Rumen, we investigated expression levels in Rumen metatranscriptome datasets. A total of 448 Rumen Bacterial genomes from the Hungate collection and Genbank, comprised of 311 Gram-positive, 136 Gram-negative and 1 Gram stain variable bacterium, were analysed. Abundance and distribution of AHL and AI-2 signalling genes showed that only one species (Citrobacter sp. NLAE-zl-C269) of a Gram-negative Bacteria appeared to possess an AHL synthase gene, while the Lux-based genes (AI-2 QS) were identified in both Gram-positive and Gram-positive Bacteria (191 genomes representing 38.2% of total genomes). Of these 192 genomes, 139 are from Gram-positive bactreetteria and 53 from Gram-negative Bacteria. We also found that the genera Butyrivibrio, Prevotella, Ruminococcus and Pseudobutyrivibrio, which are well known as the most abundant Bacterial genera in the Rumen, possessed the most lux-based AI-2 QS genes. Gene expression levels within the metatranscriptome dataset showed that Prevotella, in particular, expressed high levels of LuxS synthase suggesting that this genus plays an important role in QS within the Rumen. This is the most comprehensive study of QS in the Rumen microbiome to date. This study shows that AI-2-based QS is rife in the Rumen. These results allow a greater understanding on plant-microbe interactions in the Rumen.
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temporal metagenomic and metabolomic characterization of fresh perennial ryegrass degradation by Rumen Bacteria
Frontiers in Microbiology, 2016Co-Authors: Olga Mayorga, Michael K Theodorou, Eun Joong Kim, C J Newbold, Alison H Kingstonsmith, Gordon G Allison, Toby Wilkinson, Matthew J Hegarty, Sharon HuwsAbstract:Understanding the relationship between ingested plant material and the attached microbiome is essential for developing methodologies to improve ruminant nutrient use efficiency. We have previously shown that perennial ryegrass (PRG) Rumen Bacterial colonisation events follow a primary (up to 4 h) and secondary (after 4 h) pattern based on the differences in diversity of the attached Bacteria. In this study we investigated temporal niche specialisation of primary and secondary populations of attached Rumen microbiota using metagenomic shotgun sequencing as well as monitoring changes in the plant chemistry using mid-infrared spectroscopy (FT-IR). Metagenomic Rapid Annotation using Subsystem Technology (MG-RAST) taxonomical analysis of shotgun metagenomic sequences showed that the genera Butyrivibrio, Clostridium, Eubacterium, Prevotella and Selenomonas dominated the attached microbiome irrespective of time. MG-RAST also showed that Acidaminococcus, Bacillus, Butyrivibrio and Prevotella rDNA increased in read abundance during secondary colonisation, whilst Blautia decreased in read abundance. MG-RAST Clusters of Orthologous Groups (COG) functional analysis also showed that the primary function of the attached microbiome was categorised broadly within ‘metabolism’; predominantly amino acid, carbohydrate, and lipid metabolism and transport. Most sequence read abundances (51.6, 43.8, and 50.0% of COG families pertaining to amino acid, carbohydrate and lipid metabolism, respectively) within these categories were higher in abundance during secondary colonisation. Kyoto encyclopedia of genes and genomes (KEGG) pathways analysis confirmed that the PRG- attached microbiota present at 1 and 4 h of Rumen incubation possess a similar functional capacity, with only a few pathways being uniquely found in only one incubation time point only. FT-IR data for the plant residues also showed that the main changes in plant chemistry between primary and secondary colonisation was due to increased carbohydrate, amino acid and lipid metabolism. This study confirmed primary and secondary colonisation events and supported the hypothesis that functional changes occurred as a consequence of taxonomical changes. Sequences within the carbohydrate metabolism COG families contained only 3.2 % of cellulose activities, on average across both incubation times ( 1 and 4 h), suggesting that degradation of the plant cell walls may be a key rate- limiting factor in ensuring the bioavailability of intra-plant nutrients in
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temporal dynamics of the metabolically active Rumen Bacteria colonizing fresh perennial ryegrass
FEMS Microbiology Ecology, 2016Co-Authors: Sharon Huws, Joan E Edwards, Christopher J Creevey, Pauline Rees Stevens, Wanchang Lin, Susan E Girdwood, Justin A Pachebat, Alison H KingstonsmithAbstract:This study investigated successional colonization of fresh perennial ryegrass (PRG) by the Rumen microbiota over time. Fresh PRG was incubated in sacco in the Rumens of three Holstein × Friesian cows over a period of 8 h, with samples recovered at various times. The diversity of attached Bacteria was assessed using 454 pyrosequencing of 16S rRNA (cDNA). Results showed that plant epiphytic communities either decreased to low relative abundances or disappeared following Rumen incubation, and that temporal colonization of the PRG by the Rumen Bacteria was biphasic with primary (1 and 2 h) and secondary (4-8 h) events evident with the transition period being with 2-4 h. A decrease in sequence reads pertaining to Succinivibrio spp. and increases in Pseudobutyrivibrio, Roseburia and Ruminococcus spp. (the latter all order Clostridiales) were evident during secondary colonization. Irrespective of temporal changes, the continually high abundances of Butyrivibrio, Fibrobacter, Olsenella and Prevotella suggest that they play a major role in the degradation of the plant. It is clear that a temporal understanding of the functional roles of these microbiota within the Rumen is now required to unravel the role of these Bacteria in the ruminal degradation of fresh PRG.
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successional colonization of perennial ryegrass by Rumen Bacteria
Letters in Applied Microbiology, 2013Co-Authors: Sharon Huws, Olga Mayorga, Michael K Theodorou, L A Onime, Eun Joong Kim, A H Cookson, C J Newbold, Alison H KingstonsmithAbstract:Huws, S. A., Mayorga, O. L., Theodorou, M. K., Onime, L. A., Kim, E. J., Cookson, A. H., Newbold, C. J., Kingston-Smith, A. H. (2012). Successional colonization of perennial ryegrass by Rumen Bacteria. Letters in Applied Microbiology, 56 (3), 186-196.
Timothy J. Hackmann - One of the best experts on this subject based on the ideXlab platform.
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transport of a fluorescent analogue of glucose 2 nbdg versus radiolabeled sugars by Rumen Bacteria and escherichia coli
Biochemistry, 2016Co-Authors: Junyi Tao, César R. V. Teixeira, Rebecca K Diaz, Timothy J. HackmannAbstract:Fluorescent tracers have been used to measure solute transport, but transport kinetics have not been evaluated by comparison of radiolabeled tracers. Using Streptococcus equinus JB1 and other Bacteria, the objective of this study was to determine if a fluorescent analogue of glucose (2-NBDG) would be transported with the same kinetics and transporters as [14C]glucose. We uniquely modified a technique for measuring transport of radiolabeled tracers so that transport of a fluorescent tracer (2-NBDG) could also be measured. Deploying this technique for S. equinus JB1, we could detect 2-NDBG transport quantitatively and within 2 s. We found the Vmax of 2-NBDG transport was 2.9-fold lower than that for [14C]glucose, and the Km was 9.9-fold lower. Experiments with transport mutants suggested a mannose phosphotransferase system (PTS) was responsible for 2-NBDG transport in S. equinus JB1 as well as Escherichia coli. Upon examination of strains from 12 species of Rumen Bacteria, only the five that possessed a man...
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Transport of a Fluorescent Analogue of Glucose (2-NBDG) versus Radiolabeled Sugars by Rumen Bacteria and Escherichia coli
2016Co-Authors: Junyi Tao, Rebecca K. Diaz, César R. V. Teixeira, Timothy J. HackmannAbstract:Fluorescent tracers have been used to measure solute transport, but transport kinetics have not been evaluated by comparison of radiolabeled tracers. Using Streptococcus equinus JB1 and other Bacteria, the objective of this study was to determine if a fluorescent analogue of glucose (2-NBDG) would be transported with the same kinetics and transporters as [14C]glucose. We uniquely modified a technique for measuring transport of radiolabeled tracers so that transport of a fluorescent tracer (2-NBDG) could also be measured. Deploying this technique for S. equinus JB1, we could detect 2-NDBG transport quantitatively and within 2 s. We found the Vmax of 2-NBDG transport was 2.9-fold lower than that for [14C]glucose, and the Km was 9.9-fold lower. Experiments with transport mutants suggested a mannose phosphotransferase system (PTS) was responsible for 2-NBDG transport in S. equinus JB1 as well as Escherichia coli. Upon examination of strains from 12 species of Rumen Bacteria, only the five that possessed a mannose PTS were shown to transport 2-NBDG. Those five uniformly transported [14C]mannose and [14C]deoxyglucose (other glucose analogues at the C-2 position) at high velocities. Species that did not transport 2-NBDG at detectable velocities did not possess a mannose PTS, though they collectively possessed several other glucose transporters. These results, along with retrospective genomic analyses of previous 2-NBDG studies, suggest that only a few Bacterial transporters may display high activity toward 2-NBDG. Fluorescent tracers have the potential to measure solute transport qualitatively, but their bulky fluorescent groups may restrict (i) activity of many transporters and (ii) use for quantitative measurement
Alison H Kingstonsmith - One of the best experts on this subject based on the ideXlab platform.
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temporal metagenomic and metabolomic characterization of fresh perennial ryegrass degradation by Rumen Bacteria
Frontiers in Microbiology, 2016Co-Authors: Olga Mayorga, Michael K Theodorou, Eun Joong Kim, C J Newbold, Alison H Kingstonsmith, Gordon G Allison, Toby Wilkinson, Matthew J Hegarty, Sharon HuwsAbstract:Understanding the relationship between ingested plant material and the attached microbiome is essential for developing methodologies to improve ruminant nutrient use efficiency. We have previously shown that perennial ryegrass (PRG) Rumen Bacterial colonisation events follow a primary (up to 4 h) and secondary (after 4 h) pattern based on the differences in diversity of the attached Bacteria. In this study we investigated temporal niche specialisation of primary and secondary populations of attached Rumen microbiota using metagenomic shotgun sequencing as well as monitoring changes in the plant chemistry using mid-infrared spectroscopy (FT-IR). Metagenomic Rapid Annotation using Subsystem Technology (MG-RAST) taxonomical analysis of shotgun metagenomic sequences showed that the genera Butyrivibrio, Clostridium, Eubacterium, Prevotella and Selenomonas dominated the attached microbiome irrespective of time. MG-RAST also showed that Acidaminococcus, Bacillus, Butyrivibrio and Prevotella rDNA increased in read abundance during secondary colonisation, whilst Blautia decreased in read abundance. MG-RAST Clusters of Orthologous Groups (COG) functional analysis also showed that the primary function of the attached microbiome was categorised broadly within ‘metabolism’; predominantly amino acid, carbohydrate, and lipid metabolism and transport. Most sequence read abundances (51.6, 43.8, and 50.0% of COG families pertaining to amino acid, carbohydrate and lipid metabolism, respectively) within these categories were higher in abundance during secondary colonisation. Kyoto encyclopedia of genes and genomes (KEGG) pathways analysis confirmed that the PRG- attached microbiota present at 1 and 4 h of Rumen incubation possess a similar functional capacity, with only a few pathways being uniquely found in only one incubation time point only. FT-IR data for the plant residues also showed that the main changes in plant chemistry between primary and secondary colonisation was due to increased carbohydrate, amino acid and lipid metabolism. This study confirmed primary and secondary colonisation events and supported the hypothesis that functional changes occurred as a consequence of taxonomical changes. Sequences within the carbohydrate metabolism COG families contained only 3.2 % of cellulose activities, on average across both incubation times ( 1 and 4 h), suggesting that degradation of the plant cell walls may be a key rate- limiting factor in ensuring the bioavailability of intra-plant nutrients in
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temporal dynamics of the metabolically active Rumen Bacteria colonizing fresh perennial ryegrass
FEMS Microbiology Ecology, 2016Co-Authors: Sharon Huws, Joan E Edwards, Christopher J Creevey, Pauline Rees Stevens, Wanchang Lin, Susan E Girdwood, Justin A Pachebat, Alison H KingstonsmithAbstract:This study investigated successional colonization of fresh perennial ryegrass (PRG) by the Rumen microbiota over time. Fresh PRG was incubated in sacco in the Rumens of three Holstein × Friesian cows over a period of 8 h, with samples recovered at various times. The diversity of attached Bacteria was assessed using 454 pyrosequencing of 16S rRNA (cDNA). Results showed that plant epiphytic communities either decreased to low relative abundances or disappeared following Rumen incubation, and that temporal colonization of the PRG by the Rumen Bacteria was biphasic with primary (1 and 2 h) and secondary (4-8 h) events evident with the transition period being with 2-4 h. A decrease in sequence reads pertaining to Succinivibrio spp. and increases in Pseudobutyrivibrio, Roseburia and Ruminococcus spp. (the latter all order Clostridiales) were evident during secondary colonization. Irrespective of temporal changes, the continually high abundances of Butyrivibrio, Fibrobacter, Olsenella and Prevotella suggest that they play a major role in the degradation of the plant. It is clear that a temporal understanding of the functional roles of these microbiota within the Rumen is now required to unravel the role of these Bacteria in the ruminal degradation of fresh PRG.
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successional colonization of perennial ryegrass by Rumen Bacteria
Letters in Applied Microbiology, 2013Co-Authors: Sharon Huws, Olga Mayorga, Michael K Theodorou, L A Onime, Eun Joong Kim, A H Cookson, C J Newbold, Alison H KingstonsmithAbstract:Huws, S. A., Mayorga, O. L., Theodorou, M. K., Onime, L. A., Kim, E. J., Cookson, A. H., Newbold, C. J., Kingston-Smith, A. H. (2012). Successional colonization of perennial ryegrass by Rumen Bacteria. Letters in Applied Microbiology, 56 (3), 186-196.
Makoto Mitsumori - One of the best experts on this subject based on the ideXlab platform.
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improved culturability of cellulolytic Rumen Bacteria and phylogenetic diversity of culturable cellulolytic and xylanolytic Bacteria newly isolated from the bovine Rumen
FEMS Microbiology Ecology, 2014Co-Authors: Thet Nyonyo, Takumi Shinkai, Makoto MitsumoriAbstract:: The phylotypes of Rumen Bacteria have increased by the accumulation of 16S rRNA gene sequences, and they show a complex microbial community structure in the Rumen. However, most of the biochemical properties of Rumen Bacteria defined by phylotypes are still unknown. We attempted to improve the culturability of cellulolytic Bacteria from the Rumen using an agar medium (CA) and a gellan gum medium (CG) containing azo-carboxymethylcellulose as a carbon source. We isolated 129 strains from these media, and the numbers of isolates that showed filter paperase, carboxymethylcellulase and xylanase activity were 51, 117 and 105, respectively. The isolates were classified into six phyla by 16S rRNA gene sequences. In accordance with other studies, fibre-adherent Rumen Bacteria from the phylum Firmicutes were the most abundant cultured isolates obtained (82.2%). Isolates that were unclassified (< 97% similarity) totalled 19.4%, indicating that the media used in this study was successfully able to improve the culturability of Rumen cellulolytic Bacteria. Moreover, as the Chao1 richness of CG was higher than that of CA, we estimated that, compared with CA, CG supports the growth of a wide variety of Rumen Bacteria. These results demonstrate that culturable species of ruminal cellulolytic Bacteria can be increased using improved culture media.
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effect of media composition including gelling agents on isolation of previously uncultured Rumen Bacteria
Letters in Applied Microbiology, 2013Co-Authors: Thet Nyonyo, T Shinkai, A Tajima, Makoto MitsumoriAbstract:The aim of this study was to develop novel anaerobic media using gellan gum for the isolation of previously uncultured Rumen Bacteria. Four anaerobic media, a basal liquid medium (BM) with agar (A-BM), a modified BM (MBM) with agar (A-MBM), an MBM with phytagel (P-MBM) and an MBM with gelrite (G-MBM) were used for the isolation of Rumen Bacteria and evaluated for the growth of previously uncultured Rumen Bacteria. Of the 214 isolates composed of 144 OTUs, 103 isolates (83 OTUs) were previously uncultured Rumen Bacteria. Most of the previously uncultured strains were obtained from A-MBM, G-MBM and P-MBM, but the predominant cultural members, isolated from each medium, differed. A-MBM and G-MBM showed significantly higher numbers of different OTUs derived from isolates than A-BM (P < 0·05). The Shannon index indicated that the isolates of A-MBM showed the highest diversity (H' = 3·89) compared with those of G-MBM, P-MBM and A-BM (H' = 3·59, 3·23 and 3·39, respectively). Although previously uncultured Rumen Bacteria were isolated from all media used, the ratio of previously uncultured Bacteria to total isolates was increased in A-MBM, P-MBM and G-MBM.
Graeme T Attwood - One of the best experts on this subject based on the ideXlab platform.
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the three dimensional structure of bovine salivary protein 30b bsp30b and its interaction with specific Rumen Bacteria
PLOS ONE, 2019Co-Authors: Heng Zhang, Judith Burrows, Graeme L Card, Graeme T Attwood, Thomas T Wheeler, Vickery L ArcusAbstract:Bovine Salivary Protein 30b (BSP30b) is a member of the tubular lipid-binding (TULIP) superfamily that includes the human bactericidal/permeability-increasing proteins (BPI), lipopolysaccharide binding proteins (LBP) and palate, lung, and nasal epithelium carcinoma-associated proteins (PLUNC). BSP30b is most closely related to the PLUNC family and is predominantly found in bovine saliva. There are four BSP30 isoforms (BSP30a-d) and collectively, they are the most abundant protein component of bovine saliva. The PLUNC family members are proposed to be lipid binding proteins, although in most cases their lipid ligands are unknown. Here, we present the X-ray crystal structure of BSP30b at 2.0 A resolution. We used a double methionine mutant and Se-Met SAD phasing to solve the structure. The structure adopts a curved cylindrical form with a hydrophobic channel formed by an α/β wrap, which is consistent with the TULIP superfamily. The structure of BSP30b in complex with oleic acid is also presented where the ligand is accommodated within the hydrophobic channel. The electron density for oleic acid suggests that the ligand is only partially occupied in the binding site implying that oleic acid may not be the preferred ligand. GFP-tagged BSP30b binds to the surface of olive oil droplets, as observed under fluorescent microscopy, and acts as a surfactant consistent with its association with decreased susceptibility to bloat in cattle. Bacteria extracted directly from bovine Rumen contents indicate that the GFP_BSP30b fusion protein binds to a small number of selected Bacterial species in vivo. These results suggest that BSP30b may bind to Bacterial lipids from specific species and that this abundant protein may have important biological roles via interacting with Rumen Bacteria during feeding and rumination.
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genome sequencing of Rumen Bacteria and archaea and its application to methane mitigation strategies
Animal, 2013Co-Authors: Sinead C Leahy, William J Kelly, Eric Altermann, Ron S Ronimus, N Wedlock, Graeme T AttwoodAbstract:Ruminant-derived methane (CH4), a potent greenhouse gas, is a consequence of microbial fermentation in the digestive tract of livestock. Development of mitigation strategies to reduce CH4 emissions from farmed animals is currently the subject of both scientific and environmental interest. Methanogens are the sole producers of ruminant CH4, and therefore CH4 abatement strategies can either target the methanogens themselves or target the other members of the Rumen microbial community that produce substrates necessary for methanogenesis. Understanding the relationship that methanogens have with other Rumen microbes is crucial when considering CH4 mitigation strategies for ruminant livestock. Genome sequencing of Rumen microbes is an important tool to improve our knowledge of the processes that underpin those relationships. Currently, several Rumen Bacterial and archaeal genome projects are either complete or underway. Genome sequencing is providing information directly applicable to CH4 mitigation strategies based on vaccine and small molecule inhibitor approaches. In addition, genome sequencing is contributing information relevant to other CH4 mitigation strategies. These include the selection and breeding of low CH4-emitting animals through the interpretation of large-scale DNA and RNA sequencing studies and the modification of other microbial groups within the Rumen, thereby changing the dynamics of microbial fermentation.
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production of indolic compounds by Rumen Bacteria isolated from grazing ruminants
Journal of Applied Microbiology, 2006Co-Authors: Graeme T Attwood, D Pacheco, M H TavendaleAbstract:Aim: To screen Rumen Bacterial cultures and fresh ruminal isolates for indole and skatole production. Methods and Results: Culture collection strains and fresh Bacterial isolates from Rumen contents of sheep and dairy cows were screened for the production of indolic compounds. Clostridium aminophilum FT, Peptostreptococcus ssp. S1, Fusobacterium necrophorum D4 produced indole and Clostridium sticklandii SR produced indoleacetic acid. Fresh isolates from sheep (TrE9262 and TrE7262) and dairy cows (152R-1a, 152R-1b, 152R-3 and 152R-4) produced indole, indolepropionic acid, tryptophol and skatole from the fermentation of tryptophan and indoleacetic acid. Glucose altered the indolic compounds produced in some, but not all, isolates. TrE7262 and 152R-4 were identified as Clostridium sporogenes and 152R-1b as a new Cl. aminophilum strain. Isolates TrE9262, 152R-1a and 152R-3 were not closely related to any described species but belong to Megasphaera, Prevotella and Actinomyces genera, respectively. Conclusions: Rumen Bacteria that produced a range of indolic compounds were identified. Some isolates are distinct from the previously described Bacteria and may represent novel species. Significance and Impact of the Study: These observations will contribute to understanding skatole and indole formation in the Rumen and will lead to methods that control the formation of indolic compounds in pasture-grazed ruminants.
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the effect of condensed tannins from lotus pedunculatus and lotus corniculatus on the growth of proteolytic Rumen Bacteria in vitro and their possible mode of action
Canadian Journal of Microbiology, 2001Co-Authors: A L Molan, Graeme T Attwood, B R Min, Warren C McnabbAbstract:Five strains of proteolytic Rumen Bacteria were treated with condensed tannins (CT) purified from Lotus pedunculatus and Lotus corniculatus to investigate their effect on the growth of these bacter...
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the effect of condensed tannins from lotus pedunculatus and lotus corniculatus on the growth of proteolytic Rumen Bacteria in vitro and their possible mode of action
Canadian Journal of Microbiology, 2001Co-Authors: A L Molan, Graeme T Attwood, B R Min, Warren C McnabbAbstract:Five strains of proteolytic Rumen Bacteria were treated with condensed tannins (CT) purified from Lotus pedunculatus and Lotus corniculatus to investigate their effect on the growth of these Bacteria in vitro. Streptococcus bovis NCFB 2476, Eubacterium sp. C124b, Prevotella bryantii B14, Butyrivibrio fibrisolvens H17c, and Clostridium proteoclasticum B316T were tested against 200, 400, and 600 µg CT·mL1 extracted from L. pedunculatus and L. corniculatus. In the absence of CT, all Bacterial strains showed typical growth and reached maximum optical density (OD) after 68 h of incubation in a plant protein medium. Growth of Eubacterium sp., P. bryantii, and B. fibrisolvens was inhibited (P < 0.010.001) more by the CT from L. pedunculatus than by the CT from L. corniculatus. All strains continued to grow in the presence of 200 µg·mL1 of the CT from L. pedunculatus, but attained significantly (P < 0.050.01) lower maximum OD600 values than (minus CT) controls, except for S. bovis. At 400 and 600 µg·mL1, th...
